FILIA has been identified as a binding partner to MATER (Maternal Antigen That Embryos Require) which is encoded by a maternal effect gene. Products of each gene are detected in growing oocytes and, although transcripts are degraded prior to fertilization, the cognate proteins persist in early blastocysts. The two proteins co-localize to the cytocortex of ovulated eggs where the stability of FILIA is dependent on the presence of MATER. After fertilization, FILIA/MATER complexes become asymmetrically restricted in the apical cytocortex of two-cell embryos due to their absence in regions of cell-cell contact. This asymmetry is reversible upon disaggregation of blastomeres of the two- and four-cell embryo. Each protein persists in cells of the preimplantation embryo, but the continuous cell-cell contact of inner cells of the morulae seemingly precludes formation of the subcortical FILIA/MATER complex and results in cell populations that are marked by its presence (outer) or absence (inner). Thus, the FILIA/MATER complex provides a molecular marker of embryonic cell lineages, but it remains to be determined if the molecular asymmetry established after the first cell division plays a role in cell fate determinations in the early mouse embryo. If so, the plasticity of the FILIA/MATER complex localization may reflect the regulative nature of pre-implantation mouse development.